Here is a brief explanation of what is incorporated into the RMS and holes values in THINK:
RMS- The RMS is the root mean squares between the interaction centers of the query protein and the centers of the molecule. The precision of this value depends on the precision of the protein model, which is approximately 1 Angstrom.
Holes - The number of holes in a search corresponds to the area between the ligand and the protein, in cubic Angstroms. It is calculated by taking the volume (in the form of the grid) inside the active pocket and subtracting the volume taken up by the molecule. It has been mentioned by Find-A-Drug that the value does not seem to be indicative of false positives or false negatives in the data.
RMS- The RMS is the root mean squares between the interaction centers of the query protein and the centers of the molecule. The precision of this value depends on the precision of the protein model, which is approximately 1 Angstrom.
Holes - The number of holes in a search corresponds to the area between the ligand and the protein, in cubic Angstroms. It is calculated by taking the volume (in the form of the grid) inside the active pocket and subtracting the volume taken up by the molecule. It has been mentioned by Find-A-Drug that the value does not seem to be indicative of false positives or false negatives in the data.